Delete unneeded directory

[jabaws.git] / website / archive / binaries / mac / src / muscle / aln.cpp

diff --git a/website/archive/binaries/mac/src/muscle/aln.cpp b/website/archive/binaries/mac/src/muscle/aln.cpp
deleted file mode 100644 (file)
index 4452bc8..0000000
--- a/website/archive/binaries/mac/src/muscle/aln.cpp
+++ /dev/null
@@ -1,170 +0,0 @@
-#include "muscle.h"\r
-#include <stdio.h>\r
-#include <ctype.h>\r
-#include "msa.h"\r
-#include "textfile.h"\r
-\r
-const unsigned uCharsPerLine = 60;\r
-const int MIN_NAME = 10;\r
-const int MAX_NAME = 32;\r
-\r
-static char GetAlnConsensusChar(const MSA &a, unsigned uColIndex);\r
-\r
-void MSA::ToAlnFile(TextFile &File) const\r
-       {\r
-       if (g_bClwStrict)\r
-               File.PutString("CLUSTAL W (1.81) multiple sequence alignment\n");\r
-       else\r
-               {\r
-               File.PutString("MUSCLE ("\r
-                 SHORT_VERSION ")"\r
-                 " multiple sequence alignment\n");\r
-               File.PutString("\n");\r
-               }\r
-\r
-       int iLongestNameLength = 0;\r
-       for (unsigned uSeqIndex = 0; uSeqIndex < GetSeqCount(); ++uSeqIndex)\r
-               {\r
-               const char *ptrName = GetSeqName(uSeqIndex);\r
-               const char *ptrBlank = strchr(ptrName, ' ');\r
-               int iLength;\r
-               if (0 != ptrBlank)\r
-                       iLength = (int) (ptrBlank - ptrName);\r
-               else\r
-                       iLength = (int) strlen(ptrName);\r
-               if (iLength > iLongestNameLength)\r
-                       iLongestNameLength = iLength;\r
-               }\r
-       if (iLongestNameLength > MAX_NAME)\r
-               iLongestNameLength = MAX_NAME;\r
-       if (iLongestNameLength < MIN_NAME)\r
-               iLongestNameLength = MIN_NAME;\r
-\r
-       unsigned uLineCount = (GetColCount() - 1)/uCharsPerLine + 1;\r
-       for (unsigned uLineIndex = 0; uLineIndex < uLineCount; ++uLineIndex)\r
-               {\r
-               File.PutString("\n");\r
-               unsigned uStartColIndex = uLineIndex*uCharsPerLine;\r
-               unsigned uEndColIndex = uStartColIndex + uCharsPerLine - 1;\r
-               if (uEndColIndex >= GetColCount())\r
-                       uEndColIndex = GetColCount() - 1;\r
-               char Name[MAX_NAME+1];\r
-               for (unsigned uSeqIndex = 0; uSeqIndex < GetSeqCount(); ++uSeqIndex)\r
-                       {\r
-                       const char *ptrName = GetSeqName(uSeqIndex);\r
-                       const char *ptrBlank = strchr(ptrName, ' ');\r
-                       int iLength;\r
-                       if (0 != ptrBlank)\r
-                               iLength = (int) (ptrBlank - ptrName);\r
-                       else\r
-                               iLength = (int) strlen(ptrName);\r
-                       if (iLength > MAX_NAME)\r
-                               iLength = MAX_NAME;\r
-                       memset(Name, ' ', MAX_NAME);\r
-                       memcpy(Name, ptrName, iLength);\r
-                       Name[iLongestNameLength] = 0;\r
-\r
-                       File.PutFormat("%s      ", Name);\r
-                       for (unsigned uColIndex = uStartColIndex; uColIndex <= uEndColIndex;\r
-                         ++uColIndex)\r
-                               {\r
-                               const char c = GetChar(uSeqIndex, uColIndex);\r
-                               File.PutFormat("%c", toupper(c));\r
-                               }\r
-                       File.PutString("\n");\r
-                       }\r
-\r
-               memset(Name, ' ', MAX_NAME);\r
-               Name[iLongestNameLength] = 0;\r
-               File.PutFormat("%s      ", Name);\r
-               for (unsigned uColIndex = uStartColIndex; uColIndex <= uEndColIndex;\r
-                 ++uColIndex)\r
-                       {\r
-                       const char c = GetAlnConsensusChar(*this, uColIndex);\r
-                       File.PutChar(c);\r
-                       }\r
-               File.PutString("\n");\r
-               }\r
-       }\r
-\r
-static char GetAlnConsensusChar(const MSA &a, unsigned uColIndex)\r
-       {\r
-       const unsigned uSeqCount = a.GetSeqCount();\r
-       unsigned BitMap = 0;\r
-       unsigned Count = 0;\r
-       for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)\r
-               {\r
-               unsigned uLetter = a.GetLetterEx(uSeqIndex, uColIndex);\r
-               assert(uLetter < 32);\r
-               unsigned Bit = (1 << uLetter);\r
-               if (!(BitMap & Bit))\r
-                       ++Count;\r
-               BitMap |= Bit;\r
-               }\r
-\r
-//     '*' indicates positions which have a single, fully conserved residue\r
-       if (1 == Count)\r
-               return '*';\r
-\r
-       if (ALPHA_Amino != g_Alpha)\r
-               return ' ';\r
-\r
-#define B(a)   (1 << AX_##a)\r
-#define S2(a, b)               S(B(a) | B(b))\r
-#define S3(a, b, c)            S(B(a) | B(b) | B(c))\r
-#define S4(a, b, c, d) S(B(a) | B(b) | B(c) | B(d))\r
-#define S(w)   if (0 == (BitMap & ~(w)) && (BitMap & (w)) != 0) return ':';\r
-\r
-#define W3(a, b, c)                            W(B(a) | B(b) | B(c))\r
-#define W4(a, b, c, d)                 W(B(a) | B(b) | B(c) | B(d))\r
-#define W5(a, b, c, d, e)              W(B(a) | B(b) | B(c) | B(d) | B(e))\r
-#define W6(a, b, c, d, e, f)   W(B(a) | B(b) | B(c) | B(d) | B(e) | B(f))\r
-#define W(w)   if (0 == (BitMap & ~(w)) && (BitMap & (w)) != 0) return '.';\r
-\r
-//     ':' indicates that one of the following 'strong'\r
-// groups is fully conserved\r
-//                 STA\r
-//                 NEQK\r
-//                 NHQK\r
-//                 NDEQ\r
-//                 QHRK\r
-//                 MILV\r
-//                 MILF\r
-//                 HY\r
-//                 FYW\r
-//\r
-       S3(S, T, A)\r
-       S4(N, E, Q, K)\r
-       S4(N, H, Q, K)\r
-       S4(N, D, E, Q)\r
-       S4(M, I, L, V)\r
-       S4(M, I, L, F)\r
-       S2(H, Y)\r
-       S3(F, Y, W)\r
-\r
-//     '.' indicates that one of the following 'weaker' \r
-// groups is fully conserved\r
-//                 CSA\r
-//                 ATV\r
-//                 SAG\r
-//                 STNK\r
-//                 STPA\r
-//                 SGND\r
-//                 SNDEQK\r
-//                 NDEQHK\r
-//                 NEQHRK\r
-//                 FVLIM\r
-//                 HFY\r
-       W3(C, S, A)\r
-       W3(A, T, V)\r
-       W3(S, A, G)\r
-       W4(S, T, N, K)\r
-       W4(S, T, P, A)\r
-       W4(S, G, N, D)\r
-       W6(S, N, D, E, Q, K)\r
-       W6(N, W, Q, H, R, K)\r
-       W5(F, V, L, I, M)\r
-       W3(H, F, Y)\r
-\r
-       return ' ';\r
-       }\r